Manganese in PDB 4z7o: Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide

The structure of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide, PDB code: 4z7o was solved by F.Y.Lin, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.03 / 2.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.918, 144.524, 104.650, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.7

The structure of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide also contains other interesting chemical elements:

Calcium	(Ca)	8 atoms
Chlorine	(Cl)	1 atom

The binding sites of Manganese atom in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide (pdb code 4z7o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide, PDB code: 4z7o:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:57.5 occ:1.00 O B:HOH2116 2.0 46.8 1.0 O B:HOH2108 2.0 73.3 1.0 OD1 G:ASP410 2.1 35.3 1.0 OE2 B:GLU220 2.2 63.4 1.0 OG B:SER121 2.2 61.0 1.0 OG B:SER123 2.2 63.5 1.0 HB2 B:SER121 3.0 72.8 1.0 CB B:SER121 3.1 60.7 1.0 HB3 B:SER123 3.1 78.8 1.0 CD B:GLU220 3.2 60.8 1.0 CB B:SER123 3.2 65.7 1.0 HG3 B:GLU220 3.2 76.2 1.0 CG G:ASP410 3.3 53.5 1.0 H B:SER123 3.3 79.8 1.0 HB3 B:SER121 3.4 72.8 1.0 HA G:ASP410 3.6 79.8 1.0 CG B:GLU220 3.6 63.5 1.0 HG2 B:GLU220 3.7 76.2 1.0 HD21 B:ASN215 3.8 96.5 1.0 HB2 B:SER123 3.8 78.8 1.0 HB3 B:ALA252 3.9 0.3 1.0 OD1 B:ASP251 3.9 70.1 1.0 O B:ALA218 3.9 59.9 1.0 HB2 B:ALA252 4.0 0.3 1.0 N B:SER123 4.0 66.5 1.0 OD2 G:ASP410 4.1 60.4 1.0 CA B:SER123 4.2 67.2 1.0 CB G:ASP410 4.3 62.9 1.0 OE1 B:GLU220 4.3 58.4 1.0 OD2 B:ASP119 4.3 58.2 1.0 CA G:ASP410 4.3 66.5 1.0 CB B:ALA252 4.4 93.6 1.0 O G:HOH4001 4.4 75.0 1.0 CA B:SER121 4.4 61.8 1.0 HB2 G:ASP410 4.4 75.5 1.0 HA B:ALA218 4.4 72.6 1.0 HG2 B:MET124 4.4 75.7 1.0 ND2 B:ASN215 4.6 80.4 1.0 C B:SER121 4.7 64.0 1.0 OD1 B:ASP119 4.7 59.0 1.0 HB1 B:ALA252 4.7 0.3 1.0 H B:SER121 4.7 73.4 1.0 H B:TYR122 4.7 78.1 1.0 H B:MET124 4.8 79.7 1.0 N B:TYR122 4.8 65.1 1.0 C G:ASP410 4.8 69.4 1.0 HD22 B:ASN215 4.9 96.5 1.0 CG B:ASP119 4.9 58.5 1.0 C B:SER123 4.9 67.4 1.0 CG B:ASP251 4.9 81.4 1.0 C B:ALA218 4.9 58.7 1.0 H G:VAL411 5.0 0.9 1.0 HA B:SER123 5.0 80.6 1.0

Manganese binding site 2 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:0.7 occ:1.00 O B:HOH2172 2.1 59.0 1.0 OD2 B:ASP251 2.2 84.0 1.0 O B:SER123 2.2 68.6 1.0 O B:HOH2129 2.2 44.9 1.0 CG B:ASP251 3.2 81.4 1.0 C B:SER123 3.3 67.4 1.0 HA B:MET124 3.4 80.1 1.0 HB2 B:ASP251 3.4 0.1 1.0 OD2 B:ASP126 3.5 0.5 1.0 HB3 B:ASP251 3.6 0.1 1.0 CB B:ASP251 3.6 85.9 1.0 OD1 B:ASP127 3.7 94.7 1.0 HB2 B:SER123 3.7 78.8 1.0 N B:MET124 4.2 66.4 1.0 CA B:MET124 4.2 66.8 1.0 O B:HOH2201 4.2 46.9 1.0 OD1 B:ASP251 4.3 70.1 1.0 CA B:SER123 4.3 67.2 1.0 HA B:SER123 4.4 80.6 1.0 CB B:SER123 4.4 65.7 1.0 CG B:ASP126 4.5 0.0 1.0 H B:LYS125 4.6 94.8 1.0 SD B:MET124 4.6 63.6 1.0 OD1 B:ASP126 4.7 0.7 1.0 HG21 B:THR311 4.8 87.8 1.0 CG B:ASP127 4.8 90.1 1.0 OG B:SER123 4.8 63.5 1.0 OXT G:VAL411 4.8 84.4 1.0 HG2 B:MET124 4.9 75.7 1.0 H B:ASP126 4.9 0.8 1.0 C B:MET124 5.0 70.3 1.0 H B:MET124 5.0 79.7 1.0

Manganese binding site 3 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:91.0 occ:1.00 O B:PRO219 1.8 57.2 1.0 OD1 B:ASP217 2.1 62.7 1.0 OD1 B:ASN215 2.1 62.9 1.0 OE1 B:GLU220 2.2 58.4 1.0 OD2 B:ASP158 2.2 68.0 1.0 O B:ASP217 2.2 58.8 1.0 HA B:GLU220 2.9 81.5 1.0 C B:PRO219 3.0 55.5 1.0 CG B:ASP217 3.1 57.4 1.0 CD B:GLU220 3.3 60.8 1.0 CG B:ASN215 3.3 69.0 1.0 CG B:ASP158 3.3 61.7 1.0 C B:ASP217 3.3 59.7 1.0 HB2 B:ASP158 3.4 76.7 1.0 H B:ASP217 3.7 73.2 1.0 HD21 B:ASN215 3.7 96.5 1.0 CA B:GLU220 3.7 67.9 1.0 OD2 B:ASP217 3.7 56.2 1.0 HE2 B:HIS255 3.8 79.8 1.0 N B:GLU220 3.8 61.0 1.0 CB B:ASP158 3.9 63.9 1.0 ND2 B:ASN215 3.9 80.4 1.0 OE2 B:GLU220 4.0 63.4 1.0 C B:ALA218 4.1 58.7 1.0 N B:PRO219 4.1 57.5 1.0 CA B:ASP217 4.1 60.3 1.0 HD2 B:HIS255 4.1 68.7 1.0 HB3 B:ASP158 4.1 76.7 1.0 N B:ASP217 4.1 61.0 1.0 CA B:PRO219 4.2 56.1 1.0 CB B:ASP217 4.2 58.9 1.0 O B:ALA218 4.2 59.9 1.0 CG B:GLU220 4.3 63.5 1.0 HD2 B:PRO219 4.3 69.3 1.0 HG2 B:GLU220 4.3 76.2 1.0 HB2 B:ASN215 4.4 80.3 1.0 N B:ALA218 4.4 60.5 1.0 OD1 B:ASP158 4.4 53.6 1.0 HB3 B:TYR164 4.4 68.9 1.0 NE2 B:HIS255 4.4 66.5 1.0 CB B:GLU220 4.4 67.2 1.0 HD1 B:TYR164 4.5 67.0 1.0 CB B:ASN215 4.5 66.9 1.0 HB2 B:PRO219 4.5 66.5 1.0 CD2 B:HIS255 4.6 57.3 1.0 HB3 B:GLU220 4.6 80.6 1.0 CA B:ALA218 4.6 60.5 1.0 H B:GLU220 4.7 73.2 1.0 HA B:ALA218 4.7 72.6 1.0 HB2 B:ASP217 4.7 70.7 1.0 H B:GLY221 4.7 65.2 1.0 CD B:PRO219 4.7 57.7 1.0 HD22 B:ASN215 4.8 96.5 1.0 HB3 B:ASP217 4.9 70.7 1.0 C B:GLU220 4.9 61.1 1.0 HA B:PRO219 4.9 67.4 1.0 CB B:PRO219 4.9 55.4 1.0 HB3 B:ASN215 5.0 80.3 1.0

Manganese binding site 4 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:0.0 occ:1.00 O D:HOH2130 1.9 40.3 1.0 O D:HOH2115 2.0 48.4 1.0 OD2 I:ASP410 2.1 58.3 1.0 OE2 D:GLU220 2.1 0.5 1.0 OG D:SER121 2.2 99.2 1.0 OG D:SER123 2.2 0.7 1.0 HB2 D:SER121 2.8 0.7 1.0 CB D:SER121 3.0 98.0 1.0 H D:SER123 3.2 0.2 1.0 CD D:GLU220 3.3 0.4 1.0 CG I:ASP410 3.3 84.7 1.0 CB D:SER123 3.4 0.6 1.0 HB3 D:SER121 3.4 0.7 1.0 HA I:ASP410 3.5 0.2 1.0 HB3 D:SER123 3.5 0.7 1.0 HG3 D:GLU220 3.5 0.4 1.0 CG D:GLU220 3.9 0.0 1.0 HD21 D:ASN215 3.9 0.8 1.0 N D:SER123 4.0 0.4 1.0 OD2 D:ASP119 4.0 98.8 1.0 HB2 D:SER123 4.0 0.7 1.0 OD1 I:ASP410 4.1 91.9 1.0 CA I:ASP410 4.2 0.7 1.0 OD1 D:ASP119 4.2 98.5 1.0 HG2 D:GLU220 4.2 0.4 1.0 CB I:ASP410 4.2 0.9 1.0 HG2 D:MET124 4.2 0.5 1.0 CA D:SER121 4.3 98.8 1.0 CA D:SER123 4.3 0.4 1.0 HB3 D:ALA252 4.3 0.7 1.0 OE1 D:GLU220 4.3 99.8 1.0 HB2 D:ALA252 4.3 0.7 1.0 H D:TYR122 4.4 0.3 1.0 OD1 D:ASP251 4.4 0.7 1.0 HB2 I:ASP410 4.4 0.1 1.0 C D:SER121 4.5 0.8 1.0 CG D:ASP119 4.5 98.9 1.0 HD22 D:ASN215 4.5 0.8 1.0 O D:ALA218 4.5 96.0 1.0 C I:ASP410 4.5 0.7 1.0 N D:TYR122 4.5 0.1 1.0 H D:SER121 4.6 0.7 1.0 ND2 D:ASN215 4.6 0.5 1.0 CB D:ALA252 4.8 0.6 1.0 N I:VAL411 4.9 0.8 1.0 H I:VAL411 4.9 0.6 1.0 N D:SER121 4.9 99.0 1.0 HA D:SER121 4.9 0.6 1.0 H D:MET124 5.0 0.9 1.0

Manganese binding site 5 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:0.9 occ:1.00 OD2 D:ASP251 2.2 0.4 1.0 O D:SER123 2.2 0.8 1.0 O D:HOH2101 2.2 82.3 1.0 O D:HOH2145 2.2 59.0 1.0 HB2 D:SER123 3.0 0.7 1.0 C D:SER123 3.3 0.8 1.0 CG D:ASP251 3.3 0.2 1.0 O D:HOH2113 3.7 69.1 1.0 O I:VAL411 3.8 0.9 1.0 CB D:SER123 3.8 0.6 1.0 HA D:SER123 3.8 0.7 1.0 CA D:SER123 3.9 0.4 1.0 HA D:MET124 4.0 0.5 1.0 HB2 D:ASP251 4.1 0.7 1.0 OD1 D:ASP251 4.2 0.7 1.0 CB D:ASP251 4.2 0.1 1.0 HB3 D:ASP251 4.2 0.7 1.0 HB3 D:SER123 4.3 0.7 1.0 N D:MET124 4.4 0.6 1.0 O D:MET335 4.4 0.7 1.0 HB3 D:MET335 4.5 0.6 1.0 OD1 D:ASP127 4.7 0.9 1.0 OG D:SER123 4.7 0.7 1.0 CA D:MET124 4.7 0.9 1.0 SD D:MET124 4.8 0.7 1.0 C I:VAL411 4.9 0.7 1.0 HG2 D:MET124 5.0 0.5 1.0

Manganese binding site 6 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2003 b:0.8 occ:1.00 O D:PRO219 2.0 90.4 1.0 OD1 D:ASP217 2.1 0.6 1.0 OE1 D:GLU220 2.2 99.8 1.0 OD1 D:ASN215 2.2 0.5 1.0 OD2 D:ASP158 2.2 92.8 1.0 O D:ASP217 2.2 0.3 1.0 CG D:ASP217 3.0 0.7 1.0 HD21 D:ASN215 3.1 0.8 1.0 CG D:ASN215 3.1 0.7 1.0 C D:PRO219 3.2 90.1 1.0 HA D:GLU220 3.2 0.6 1.0 C D:ASP217 3.2 99.9 1.0 CD D:GLU220 3.3 0.4 1.0 CG D:ASP158 3.4 91.8 1.0 ND2 D:ASN215 3.4 0.5 1.0 OD2 D:ASP217 3.5 95.5 1.0 HB2 D:ASP158 3.6 0.1 1.0 H D:ASP217 3.7 0.7 1.0 CA D:ASP217 3.9 0.6 1.0 N D:ASP217 4.0 0.6 1.0 CA D:GLU220 4.0 98.0 1.0 HE2 D:HIS255 4.0 0.5 1.0 OE2 D:GLU220 4.0 0.5 1.0 N D:GLU220 4.0 99.0 1.0 C D:ALA218 4.0 95.8 1.0 CB D:ASP217 4.0 0.1 1.0 CB D:ASP158 4.0 91.7 1.0 N D:PRO219 4.1 93.6 1.0 O D:ALA218 4.1 96.0 1.0 HD2 D:PRO219 4.2 0.9 1.0 CA D:PRO219 4.2 91.5 1.0 N D:ALA218 4.3 97.5 1.0 HD22 D:ASN215 4.3 0.8 1.0 HB3 D:ASP158 4.3 0.1 1.0 OD1 D:ASP158 4.4 91.0 1.0 CB D:ASN215 4.4 1.0 1.0 HD1 D:TYR164 4.5 0.3 1.0 CG D:GLU220 4.5 0.0 1.0 HB2 D:ASN215 4.5 0.6 1.0 HB2 D:ASP217 4.5 0.7 1.0 NE2 D:HIS255 4.6 88.7 1.0 CA D:ALA218 4.6 98.3 1.0 HG2 D:GLU220 4.6 0.4 1.0 HD2 D:HIS255 4.6 0.7 1.0 HA D:ALA218 4.7 1.0 1.0 CB D:GLU220 4.7 94.9 1.0 HB2 I:ASP410 4.7 0.1 1.0 CD D:PRO219 4.7 93.3 1.0 HB3 D:ASP217 4.7 0.7 1.0 H D:ARG216 4.7 0.7 1.0 HB2 D:PRO219 4.8 0.9 1.0 HB3 D:GLU220 4.8 0.9 1.0 HB3 D:TYR164 4.8 0.6 1.0 C D:ARG216 4.8 98.8 1.0 HB3 D:ASN215 4.8 0.6 1.0 H D:GLU220 4.8 0.8 1.0 HA D:ASP217 4.9 0.7 1.0 H D:GLY221 4.9 0.9 1.0 CD2 D:HIS255 4.9 83.9 1.0 HA D:PRO219 4.9 0.8 1.0

F.Y.Lin, J.Zhu, E.T.Eng, N.E.Hudson, T.A.Springer. Beta-Subunit Binding Is Sufficient For Ligands to Open the Integrin Alpha Iib Beta 3 Headpiece. J.Biol.Chem. V. 291 4537 2016.
ISSN: ESSN 1083-351X
PubMed: 26631735
DOI: 10.1074/JBC.M115.705624